
Please feel free to contact me at tshibuya 'at-mark' hgc 'dot' jp to request
copies of papers whose files are not provided.
Refereed Journal Papers
- Akito Yamamoto, Tetsuo Shibuya, Privacy-Preserving Statistical Analysis
of Genomic Data using Compressive Mechanism with Haar Wavelet Transform,
Journal of Computational Biology, in press.
- Akito Yamamoto, Tetsuo Shibuya, More practical differentially private publication
of key statistics in GWAS, Bioinformatics Advances, Bioinformatics Advances,
Volume 1, Issue 1, vbab004, 2021. https://doi.org/10.1093/bioadv/vbab004
- Yao-zhong Zhang, Arda Akdemir, Georg Tremmel, Seiya Imoto, Satoru Miyano,
Tetsuo Shibuya, and Rui Yamaguchi, Nanopore basecalling from a perspective
of instance segmentation, BMC Bioinformatics, 21, Article number:136, April
2020. https://doi.org/10.1186/s12859-020-3459-0
- Tetsuo Shibuya, Application-Oriented Succinct Data Structures for Big Data,
The Review of Socionetwork Strategies, 13, pp. 227–236, 9 Oct, 2019. https://doi.org/10.1007/s12626-019-00045-1
- Yoichi Sasaki, Tetsuo Shibuya, Kimihito Ito, and Hiroki Arimura, Efficient
Approximate 3-Dimensional Point Set Matching Using Root-Mean-Square Deviation
Score, IEICE Transactions on Fundamentals, E102.A(9), pp. 1159-1170, Sept
1, 2019. https://doi.org/10.1587/transfun.E102.A.986
- Ritsuko Onuki, Rui Yamaguchi, Tetsuo Shibuya, Minoru Kanehisa, and Susumu
Goto, Revealing Phenotype-Associated Functional Differences by Genome-Wide
Scan of Ancient Haplotype Blocks, PLOS ONE, 12(4): e0176530, April 26,
2017, https://doi.org/10.1371/journal.pone.0176530.
- Kiyoshi Yamaguchi, Satoshi Nagayama, Eigo Shimizu, Mitsuhiro Komura, Rui
Yamaguchi, Tetsuo Shibuya, Masami Arai, Seira Hatakeyama, Tsuneo Ikenoue,
Masashi Ueno, Satoru Miyano, Seiya Imoto, Yoichi Furukawa, Reduced expression
of APC-1B but not APC-1A by the deletion of promoter 1B is responsible
for familial adenomatous polyposis, Scientific Reports 6, Article number:
26011, 2016, doi:10.1038/srep26011.
- Akihiro Fujimoto, Mayuko Furuta, Yasushi Totoki, Tatsuhiko Tsunoda, Mamoru
Kato, Yuichi Shiraishi, Hiroko Tanaka, Hiroaki Taniguchi, Yoshiiku Kawakami,
Masaki Ueno, Kunihito Gotoh, Shun-ichi Ariizumi, Christopher P Wardell,
Shinya Hayami, Toru Nakamura,Hiroshi Aikata, Koji Arihiro, Keith A Boroevich,
Tetsuo Abe, Kaoru Nakano, Kazuhiro Maejima, Aya Sasaki-Oku, Ayako Ohsawa,
Tetsuo Shibuya, Hiromi Nakamura, Natsuko Hama, Fumie Hosoda, Yasuhito Arai,
Shoko Ohashi, Tomoko Urushidate, Genta Nagae, Shogo Yamamoto, Hiroki Ueda,
Kenji Tatsuno, Hidenori Ojima, Nobuyoshi Hiraoka, Takuji Okusaka, Michiaki
Kubo, Shigeru Marubashi, Terumasa Yamada, Satoshi Hirano, Masakazu Yamamoto,
Hideki Ohdan, Kazuaki Shimada, Osamu Ishikawa, Hiroki Yamaue, Kazuki Chayama,
Satoru Miyano, Hiroyuki Aburatani, Tatsuhiro Shibata, and Hidewaki Nakagawa,
"Whole-genome mutational landscape and characterization of noncoding
and structural mutations in liver cancer", Nature Genetics 48, 500–509,
April 2016. doi:10.1038/ng.3547.
- Wing-Kin Sung, Kunihiko Sadakane, Tetsuo Shibuya, Abha Belorkar and Iana
Pyrogova, An O(m log m)-time algorithm for detecting superbubbles, IEEE/ACM
Transactions on Computational Biology and Bioinformatics, 12(4), pp. 770-777,
July/August 2015. doi:10.1109/TCBB.2014.2385696
- Yoichi Furukawa, Kiyoshi Yamaguchi, Mitsuhiro Komura, Rui Yamaguchi, Seiya
Imoto, Eigo Shimizu, Shinichi Kasuya, Tetsuo Shibuya, Seira Hatakeyama,
Norihiko Takahashi, Tsuneo Ikenoue, Keisuke Hata, Giichiro Tsurita, Masaru
Shinozaki, Yutaka Suzuki, Sumio Sugano, and Satoru Miyano. Detection of
APC mosaicism by next-generation sequencing in an FAP patient. Journal
of Human Genetics, 60(5), pp. 227-231, DOI: 10.1038/jhg.2015.14, May 2015.
- Yoichi Furukawa, Tsuneo Ikenoue, Kiyoshi Yamaguchi, Mitsuhiro Komura, Seiya Imoto, Rui Yamaguchi, Eigo Shimizu, Shinichi Kasuya, Tetsuo Shibuya, Seira Hatakeyama, and Satoru Miyano, Attenuated Familial Adenomatous Polyposis with Desmoids by an APC Mutation. Human Genome Variation, vol. 2, Article number: 15011, doi:10.1038/hgv.2015.11, 26 March 2015.
- Akihiro Fujimoto, Mayuko Furuta, Yuichi Shiraishi, Ha Nguyen, Daichi Shigemizu,
Kunihito Gotoh, Yoshiiku Kawakami, Toru Nakamura, Masaki Ueno, Shun-ichi
Ariizumi, Tatstuhiro Shibata, Tetsuo Abe, Keith Boroevich, Kaoru Nakano,
Aya Sasaki, Rina Kitada, Kazihiro Maejima, Hiroko Tanaka, Tetsuo Shibuya,
Hidenori Ojima, Kazuaki Shimada, Shinya Hayami, Yoshinobu Shigekawa, Hiroshi
Aikata, Koji Arihiro, Hideki Ohdan, Shigeru Marubashi, Terumasa Yamada,
Osamu Ishikawa, Michiaki Kubo, Satoshi Hirano, Masakazu Yamamoto, Hiroki
Yamaue, Kazuaki Chayama, Satoru Miyano, Tatsuhiko Tsunoda, and Hidewaki
Nakagawa. Whole-genome mutational landscape of liver cancers displaying
biliary phenotype reveals hepatitis impact and molecular diversity, Nature
Communications 6, Article No. 6120, doi:10.1038/ncomms7120, 30 January
2015.
- Yuichi Shiraishi, Akihiro Fujimoto, Mayuko Furuta, Hiroko Tanaka, Ken-ichi
Chiba, Keith A Boroevich, Tetsuo Abe, Yoshi-iku Kawakami, Masaki Ueno,
Kunihito Gotoh, Shun-ichi Ariizumi, Tetsuo Shibuya, Kaoru Nakano, Aya Sasaki,
Kazuhiro Maejima, Rina Kitada, Shinya Hayami, Yoshinobu Shigekawa, Shigeru
Marubashi, Terumasa Yamada, Michiaki Kubo, Osamu Ishikawa, Hiroshi Aikata,
Koji Arihiro, Hideki Ohdan, Masakazu Yamamoto, Hiroki Yamaue, Kazuaki Chayama,
Tatsuhiko Tsunoda, Satoru Miyano, and Hidewaki Nakagawa, Integrated analysis
of whole genome and transcriptome sequencing reveals diverse transcriptomic
aberrations driven by somatic genomic changes in liver cancers, PLoS ONE
9(12): e114263. doi:10.1371/journal.pone.0114263, December 2014.
- Akihiro Fujimoto, Yasushi Totoki, Tetsuo Abe, Keith A Boroevich, Fumie
Hosoda, Ha Hai Nguyen, Masayuki Aoki, Naoya Hoshono, Michiaki Kubo, Fuyuki
Miya, Yasuhito Arai, Hiroyuki Takahashi, Takuya Shirakihara, Masao Nagasaki,
Tetsuo Shibuya, Kaoru Nakano, Kumiko Watanabe-Makino, Hiroko Tanaka, Hiromi
Nakamura, Jun Kusuda, Hidenori Ojima, Kazuaki Shimada, Takuji Okusaka,
Masaki Ueno, Yoshinobu Shigekawa, Yoshiiku Kawakami, Koji Arihiro, Hideki
Ohdan, Kunihito Gotoh, Osamu Ishikawa, Shun-ichi Ariizumi, Masakazu Yamamoto,
Terumasa Yamada, Kazuaki Chayama, Tomoo Kosuge, Hiroki Yamaue, Naoyuki
Kamatani, Satoru Miyano, Hitoshi Nakagama, Yusuke Nakamura, Tatsuhiko Tsunoda,
Tatsuhiro Shibata, and Hidewaki Nakagawa. Whole Genome Sequencing of Liver
Cancers Identifies Etiological Influences on Mutation Patterns and Recurrent
Mutations in Chromatin Regulators. Nature Genetics, Vol. 44, pp. 760-764,
2012.
- Mohammed Sahli and Tetsuo Shibuya, Arapan-S: A Fast and Highly Accurate
Whole-Genome Assembly Software for Viruses and Small Genomes, BMC Research
Notes, 5:243, doi:10.1186/1756-0500-5-243, 2012.
- Genki Terashi, Tetsuo Shibuya, and Mayuko Takeda-Shitaka, LB3D: a protein
3D substructure search program based on the lower bound of a RMSD value,
Journal of Computational Biology, Vol. 19, No. 5, pp. 493-503, 2012.
- Mohammed Sahli and Tetsuo Shibuya, Max-Shift BM and Max-Shift Horspool:
Practical Fast Exact String Matching Algorithms. Journal of Information
Processing, Vol. 53, No. 4, 2012.
- Ritsuko Onuki, Ryo Yamada, Rui Yamaguchi, Minoru Kanehisa, and Tetsuo Shibuya,
Population Model-Based Inter-Diplotype Similarity Measure for Accurate
Diplotype Clustering, Journal of Computational Biology, Vol. 19, No 1,
pp. 55-67, 2012. (journal site)
- Mohammed Sahli and Tetsuo Shibuya, Removing vector sequences from shotgun
raw data. Journal of Biotechnology, Bioinformatics and Bioengineering,
Vol. 4, pp. 431-441, 2011.
- Akihiro Fujimoto, Hidewaki Nakagawa, Naoya Hosono, Kaoru Nakano, Tetsuo Abe, Keith A Boroevich, Masao Nagasaki, Rui Yamaguchi, Tetsuo Shibuya, Michiaki Kubo, Satoru Miyano, Yusuke Nakamura, and Tatsuhiko Tsunoda. Whole-genome Sequencing and Comprehensive Variant Analysis of a Japanese Individual Using Massively Parallel Sequencing, Nature Genetics, Vol. 42, pp. 931-936, 2010. (journal site)
- Tetsuo Shibuya, Searching Protein 3-D Structures in Faster Than Linear
Time, Journal of Computational Biology, Vol. 17, No. 4, pp. 593-602, 2010.
(preprint) (journal site)
- Tetsuo Shibuya, Fast Hinge Detection Algorithms for Flexible Protein Structures,
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol.
7, No. 2, 2010, pp. 333-341. (preprint) (journal site) (IPSJ Yamashita SIG Research Award, March 11, 2009)
- Tetsuo Shibuya, Searching Protein 3-D Structures in Linear Time, Journal
of Computational Biology, Vol. 17, No. 3, pp. 203-219, 2010. (Preliminary
version has appeared in RECOMB '09) (journal site)
- Tetsuo Shibuya, Geometric Suffix Tree: Indexing Protein 3-D Structures,
Journal of the ACM, Vol. 57, No. 3, Article No.15, pp. 1-17, 2010.(ACM portal)
- Tetsuo Shibuya, Jesper Jansson, and Kunihiko Sadakane, Linear-Time Protein
3-D Structure Searching with Insertions and Deletions, BMC Algorithms for
Molecular Biology, Vol. 5:7, 2010. (journal site) (PDF file at the journal site)
- Ben Hachimori and Tetsuo Shibuya, Lazy Suffix Array: The Data Structure
for Online Construction and Pattern Searching, IEICE Transactions on Fundamentals,
Vol. E92-A, No. 8, pp. 1750-1756, 2009. (J-Stage)
- Tetsuo Shibuya, Efficient Substructure RMSD Query Algorithms, Journal of Computational Biology, Vol. 14, No. 9, pp. 1201-1207, 2007. (journal site) (preprint)
- Tetsuo Shibuya, Generalization of a Suffix Tree for RNA Structural Pattern
Matching, Algorithmica, Vol. 39, No. 1, pp. 1 - 19, 2004. (journal site) (preprint)
- Tetsuo Shibuya, Hisashi Kashima, and Akihiko Konagaya, Efficient Filtering
Methods for Clustering cDNAs with Spliced Sequence Alignment, Bioinformatics,
Vol. 20, pp. 29-39, 2004. (journal site)
- Eain Murphy, Isidore Rigoutsos, Tetsuo Shibuya, and Thomas Shenk, Re-evaluation
of Human Cytomegalovirus Coding Potential, Proceedings of the National
Academy of Sciences, Vol. 100, No. 23, pp. 13585-13590, 2003. (journal site)
- Tien Huynh, Isidore Rigoutsos, Laxmi Parida, Daniel Platt, and Tetsuo Shibuya,
The IBM Bioinformatics Group Web Server - Tools and Content, Nucleic Acids
Research, Vol. 31, No. 13, pp. 3645-3650, 2003. (journal site)
- Tetsuo Shibuya, Constructing the Suffix Tree of a Tree with a Large Alphabet,
IEICE Transactions on Fundamentals of Electronics, Communications and Computer
Sciences, Vol. E86-A, No.5, pp. 1061-1066, May 2003. (journal site) (PDF file)
- Tetsuo Shibuya and Isidore Rigoutsos, Dictionary-driven Prokaryotic Gene Finding, Nucleic Acids Research, Vol. 30, pp. 2710-2725, 2002. (journal site) (PDF file)
- Hiroshi Kawazoe, Tetsuo Shibuya, and Takeshi Tokuyama, Optimal On-line
Algorithms for an Electronic Commerce Money Distribution System, Algorithmica,
Vol. 33, pp. 287-299, 2002. (journal site) (preprint)
- Tetsuo Shibuya, Computing the n x m Shortest Paths Efficiently, The ACM
Journal of Experimental Algorithmics, ISSN 1084-6654, Vol. 5, No. 9, 2000.
(journal site) (PDF file)
- Tetsuya Ueda, Hiroki Sasaki, Yoshitaka Kuwahara, Masahiko Nezu, Tetsuo
Shibuya, Hiromi Sakamoto, Kazuyoshi Yanagihara, Kennichi Mafune, Masatoshi
Makuuchi, and Masaaki Terada, Deletion of the Carboxyl-Terminal Exons of
K-sam/FPGR2 by Short Homology-Mediated Recombination, Generating Preferential
Expression of Specific mRNAs, Cancer Research, Vol. 59, No. 24, pp. 6080-6086,
Dec 15, 1999. (journal site)
- Tetsuo Shibuya, Hiroshi Imai, Shigeki Nishimura, Hiroshi Shimoura, and
Kenji Tenmoku, Finding Useful Detours in Geographical Databases, IEICE
Transactions on Information and Systems, Vol. E82-D, No. 1, pp. 282-290,
January 1999. (journal site) (PDF file)
- Tetsuo Shibuya and Hiroshi Imai, New Flexible Approaches for Multiple Sequence
Alignment, Journal of Computational Biology, Vol. 4, No. 3, Mary Ann Liebert,
Inc., pp. 385-413, 1997. (preprint)
Refereed Conference Papers
- Akito Yamamoto, Eizen Kimura, and Tetsuo Shibuya, (epsilon, k)-Randomized
Anonymization: epsilon-Differentially Private Data Sharing with k-Anonymity,
The 16th International Conference on Health Informatics (HEALTHINF 2023),
Lisbon, Portugal, February 16-18, 2023, to appear.
- Robert Barish, Tetsuo Shibuya, Hardness of bounding influence via graph
modification, Proc. 48th International Conference on Current Trend in Theory
and Practice of Computer Science, Novy Smokovec, Slovakia, January 15-19,
2023, LNCS, to appear.
- Robert Barish, Tetsuo Shibuya, String editing under pattern constraints,
Proc. Workshop on Algorithms, Bioinformatics, and Computation Theory, International
Computer Symposium, December 15-17, 2022, Taoyuan, Taiwan, 2022, to appear.
- Akito Yamamoto, Tetsuo Shibuya, Efficient and Highly Accurate Differentially Private Statistical Genomic Analysis using Discrete Fourier Transform, The 21st IEEE International Conference on Trust, Security and Privacy in Computing and Communications (IEEE TrustCom 2022), Wuhan, China, October 28-30, 2022, to appear. (IEEE Outstanding Paper Award)
- Robert Barish, Tetsuo Shibuya, Counting on a rainbow connection, Italian Conference on Theoretical Computer Science, 7-9 September, 2022, Rome, Italy.
- Robert Barish, Tetsuo Shibuya, Proper colorability of segment intersection
graphs, The 28th International Computing and Combinatorics Conference (COCOON
2022), 2022, Shenzhen, China, October 22-24, 2022, to appear.
- Robert Barish, Tetsuo Shibuya, Optimally Confining Lattice Polymers, Proc.
Canadian Conference on Computational Geometry, August 25-27, 2022, Tronto,
Canada, pp.24-31.
- Akito Yamamoto, Tetsuo Shibuya, Privacy-Preserving Statistical Analysis
of Genomic Data using Compressive Mechanism with Haar Wavelet Transform,
RECOMB Privacy and Security Workshop, 2022, to appear.
- Arda Akdemir, Yeojoo Jeon and Tetsuo Shibuya, Developing Language Resources
and NLP Tools for the North Korean Language, Proc. 13th Conference on Language
Resources and Evaluation (LREC 2022), June 20-25, 2022, pp. 5595‑5600.
- Akito Yamamoto, Tetsuo Shibuya, Efficient Differentially Private Methods
for a Transmission Disequilibrium Test in Genome Wide Association Studies,
PACIFIC SYMPOSIUM ON BIOCOMPUTING 2022, pp. 85--96.
- Akito Yamamoto, Tetsuo Shibuya, Differentially Private Linkage Analysis
with TDT --- the case of two affected children per family, 2021 IEEE International
Conference on Bioinformatics and Biomedicine (BIBM), 2021, pp. 765-770.
- Arda Akdemir, Tetsuo Shibuya, UDON: Unsupervised Data SelectiON for Biomedical
Entity Recognition, Proc. 4th International Conference on Computing and
Big Data, 2021, pp. 1–7. (Best Oral Presentation Award)
- Robert Barish and Tetsuo Shibuya, Solving teleportation mazes with limited
visibility, The 23rd Thailand-Japan Conference on Discrete and Computational
Geometry, Graphs, and Games, pp.110-111, 2021.
- Kazushi Kitaya and Tetsuo Shibuya, Compression of Multiple k-mer Sets by
Iterative SPSS Decomposition, Proc. WABI 2021, Leibniz International Proceedings
in Informatics (LIPIcs), vol. 201(12), pp.1-12, 2021.
- Arda Akdemir, Tetsuo Shibuya, and Tunga Güngör. Subword Contextual Embeddings
for Languages with Rich Morphology, ICMLA 2020, full paper, 2020, pp. 994-1001.
- Taku Onodera, Tetsuo Shibuya, Wear Leveling Revisited, The 31st International
Symposium on Algorithms and Computation, Leibniz International Proceedings
in Informatics (LIPIcs) 181(65):1-65:17. 2020. Dec 4.
- Arda Akdemir, Tetsuo Shibuya, Transfer Learning for Biomedical Question
Answering. CLEF 2020. Proceedings Publication Date: September 2020
- Taku Onodera, Tetsuo Shibuya. Succinct Oblivious RAM, Proc. Symposium on
Theoretical Aspects of Computer Science (STACS 2018), vol.96, pp. 52:1–52:16,
2018. 10.4230/LIPIcs.STACS.2018.52 (Proceedings paper) (full version on arXiv)
- Taku Onodera, Tetsuo Shibuya, Fast Classification of Protein Structures by an Alignment-free Kernel, The 23rd International Symposium on String Processing and Information Retrieval (SPIRE 2016), LNCS 9954, pp. 68-79, October 18-20, Beppu, Japan, 2016, DOI: 10.1007/978-3-319-46049-9_7
- Yang Li, Tetsuo Shibuya, Malphite: A Convolutional Neural Network and Ensemble
Learning Based Protein Secondary Structure Predictor, IEEE International
Conference on Bioinformatics and Biomedicine (BIBM), November 2015, pp.
1260-1266, IEEE Press, ISBN 978-1-4673-6799-8/15. doi:10.1109/BIBM.2015.7359861
- Yoichi Sasaki, Tetsuo Shibuya, Kimihito Ito, and Hiroki Arimura, Efficient
Approximate 3-Dimensional Point Set Matching Using Root-Mean-Square Deviation
Score, 8th International Conference on Similarity Search and Applications
(SISAP 2015), October 12-14, Glasgow, Scotland, UK, 2015, LNCS 9371, pp.
191-203 (DOI: 10.1007/978-3-319-25087-8_18).
- Mohammad A. Eita, Tetsuo Shibuya, and Amin A. Shoukry, Locating Controlling
Regions of Neural Networks Using Constrained Evolutionary Computation,
2015 IEEE Congress on Evolutionary Computation (CEC2015), pp. 1581-1588,
IEEE Press, ISBN 978-1-4799-7492-4/1, 2015, Sendai, Japan.
- Tomohiko Ohtsuki, Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yukuto
Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Tetsuo Shibuya and Masao Nagasaki,
SVEM: a Structural Variant Estimation Method using Multi-Mapped Reads on
Breakpoints, 1st International Conference on Algorithms for Computational
Biology (AlCoB 2014), 2014, LNBI 8542, pp 208-219, 2014.
- Sherin Moustafa El Gokhy, Tetsuo Shibuya and Amin Shoukry, Improving miRNA
Classification Using an Exhaustive Set of Features, The 8th International
Conference on Practical Applications of Computational Biology and Bioinformatics
(PACBB 2014), Advances in Intelligent Systems and Computing, Springer,
Vol. 294, pp 31-39, 2014. (DOI: 10.1007/987-3-319-07581-5_4)
- Taku Onodera, Kunihiko Sadakane and Tetsuo Shibuya, Detecting Superbubbles
in Assembly Graphs, The 13th Workshop on Bioinformatics (WABI 2013), LNCS
8126, pp. 338-348, 2013.
- Taku Onodera, Tetsuo Shibuya, The Gapped Spectrum Kernel for Support Vector
Machines, Proc. Machine Learning and Data Mining (MLDM 2013), LNCS 7988,
pp. 1-15, 2013.
- Alexander Bowe, Taku Onodera, Kunihiko Sadakane and Tetsuo Shibuya, Succinct
de Bruijn Graphs, The 12th Workshop on Algorithms in Bioinformatics (WABI
2012), LNCS 7534, pp. 225-235, 2012.
- Mohammed Sahli and Tetsuo Shibuya, Argan - an artificial sequencing tool
for simulated data, The 4th International Conference on Bioinformatics
and Biomedical Technology (ICBBT 2012), Vol. 29, pp. 196-199, 2012. (conference site)
- Mohammed Sahli and Tetsuo Shibuya, An algorithm for classifying DNA reads,
International Conference on Bioscience, Biochemistry and Bioinformatics
(ICBBB 2012), Vol. 31, pp. 59-63, 2012. (conference site)
- Mohammed Sahli and Tetsuo Shibuya, Qamar - A More Accurate DNA Sequencing
Error Correcting Algorithm, International Conference on Bioscience, Biochemistry
and Bioinformatics (ICBBB 2012), Vol. 31, pp. 53-58, 2012. (conference site)
- Taku Onodera and Tetsuo Shibuya, An Index Structure for Spaced Seed Search,
Proc. 22nd annual International Symposium on Algorithms and Computation
(ISAAC 2011), LNCS, vol. 7074, pp. 764-772, 2011.
- Daisuke Kimura, Tetsuji Kuboyama, Tetsuo Shibuya, and Hisashi Kashima,
A Subpath Kernel for Rooted Unordered Trees, Proc. The 15th Pacific-Asia
Conference on Knowledge Discovery and Data Mining (PAKDD 2011), pp. 62-74,
2011. (Accepted as a long presentation paper)
- Tetsuo Shibuya, Jesper Jansson and Kunihiko Sadakane, Linear-Time Protein
3-D Structure Searching with Insertions and Deletions, 9th Workshop on
Algorithms in Bioinformatics (WABI 2009), LNCS, vol. 5724, pp. 310-320,
2009. (PDF file)
- Ritsuko Onuki, Tetsuo Shibuya and Minoru Kanehisa, New Kernel Methods for
Phenotype Prediction from Genotype Data, Proc. 9th Annual Workshop on Bioinformatics
and Systems Biology (IBSB), Genome Informatics, Vol. 22, pp. 132-141, 2009.
(PDF file)
- Tetsuo Shibuya, Searching Protein 3-D Structures in Linear Time, Proc.
13th Annual International Conference on Research in Computational Molecular
Biology (RECOMB 2009), LNCS 5817 (LNBI 5541), pp. 1-15, 2009. (PDF file) (Best Paper Award)
- Tetsuo Shibuya, Prefix-Shuffled Geometric Suffix Tree, Proc. 14th String
Processing and Information Retrieval Symposium (SPIRE 2007), LNCS 4726,
pp. 300-309, 2007. (PDF file)
- Tetsuo Shibuya, Geometric Suffix Tree: A New Index Structure for Protein
3-D Structures, Proc. Combinatorial Pattern Matching 2006 (CPM 2006), LNCS
4009, pp. 84-93, 2006. (PDF file)
- Hiroki Sakai, Hiroo Murakami, Sachiyo Aburatani, Tetsuo Shibuya, Katsuhisa
Horimoto, and Minoru Kanehisa, Bayesian Approach for Sequence Pattern Search
in Tissue Specific Alternative Splicing, Proc. 9th World Multi-Conference
on Systemics, Cybernetics and Informatics, Vol. 3, pp. 25-30, 2005.
- Tetsuo Shibuya and Igor Kurochkin, Match Chaining Algorithms for cDNA Mapping.
Proc. Algorithms in Bioinformatics (WABI'03), LNCS 2182, pp. 462-473, 2003.
(PDF file)
- Kunihiko Sadakane and Tetsuo Shibuya, Indexing Huge Genome Sequences for
Solving Various Problems. Genome Informatics, Vol. 12, pp. 175-183, 2001.
(PDF file)
- Tetsuo Shibuya, Generalization of a Suffix Tree for RNA Structural Pattern
Matching, Proc. 7th Scandinavian Workshop on Algorithm Theory (SWAT'00),
LNCS 1851, pp. 393-406, 2000.
- Tetsuo Shibuya, Constructing the Suffix Tree of a Tree with a Large Alphabet,
Proc. 10th annual International Symposium on Algorithms and Computation
(ISAAC'99), LNCS 1741, pp. 225-236, 1999.
- Tetsuo Shibuya, Computing the n x m Shortest Paths Efficiently, Proc. 1st
International Workshop on Algorithm Engineering and Experimentation (ALENEX'99),
LNCS 1619, pp. 210-225, 1999.
- Hiroshi Kawazoe, Tetsuo Shibuya, and Takeshi Tokuyama, Optimal On-line
Algorithms for an Electronic Commerce Money Distribution System, Proc.
10th ACM-SIAM Symposium on Discrete Algorithms (SODA 99), pp. 527-536,
1999.
- Tetsuo Shibuya and Hiroshi Imai, New Flexible Approaches for Multiple Sequence
Alignment, Proc. 1st Annual International Conference on Computational Molecular
Biology (RECOMB '97), pp. 267-276, 1997.
- Tetsuo Shibuya and Hiroshi Imai, Enumerating Suboptimal Alignments of Multiple
Biological Sequences Efficiently, Proc. Pacific Symposium on Biocomputing
'97, pp. 409-420, 1997.
- Tetsuo Shibuya and Hiroshi Imai, Parametric Alignment of Multiple Biological
Sequences, Genome Informatics, Vol 7, pp. 41-50, 1996.
- Tetsuo Shibuya, Hiroshi Imai, Shigeki Nishimura, Hiroshi Shimoura, and
Kenji Tenmoku, Detour Queries in Geographical Databases for Navigation
and Related Algorithm Animations, Proc. International Symposium on Cooperative
Database Systems for Advanced Applications (CODAS'96), Vol. 2, pp. 333-340,
1996.
- Tsuyoshi Ono, Yoshiaki Kyoda, Tomonari Masada, Kazuyoshi Hayase, Motoki
Nakade, Kunihiko Sadakane, Tetsuo Shibuya, Mary Inaba, Hiroshi Imai, Keiko
Imai, and David Avis, A Package for Traiangulations. Proc. 12th Annual
ACM Symposium on Computational Geometry, pp. V17-V18, 1996.
- Tetsuo Shibuya, Takahiro Ikeda, Hiroshi Imai, Shigeki Nishimura, Hiroshi
Shimoura, and Kenji Tenmoku, Finding a Realistic Detour by AI Search Techniques,
Proc. 2nd Intelligent Transportation Systems, Vol. 4, pp. 2037-2044, 1995.
Books
- Akdemir A., Shibuya T., Güngör T. (2022) A Comprehensive Analysis of Subword
Contextual Embeddings for Languages with Rich Morphology. In: Wani M.A.,
Raj B., Luo F., Dou D. (eds) Deep Learning Applications, Volume 3. Advances
in Intelligent Systems and Computing, vol 1395. Springer, Singapore, pp.
31-72.
- Tetsuo Shibuya, Algorithms, Maruzen, 2016. (In Japanese. See my Japanese publication list)
- Kengo Kinoshita, Tetsuo Shibuya, and Kenta Nakai, "Computational Biology",
Gendai Suuri Kagaku Jiten, Heisuke Hiranaka eds., 2009, .pp. 342-354. (In
Japanese. See my Japanese publication list)
- Neil C.Jones and Pavel Pevzner, Introduction to Bioinformatics Algorithms, translated to Japanese by Tetsuo Shibuya and Hideo Bannai, 2007. (publisher's site) (Japanese Translation. See my Japanese publication list)
- Kenta Nakai, et al. eds., Encyclopedia of Bioinformatics, Kyoritsu Shuppan,
2006. (In Japanese, as an editor and an author, , see my Japanese publication list). (publisher's site)
- Tetsuo Shibuya, Basics of Datamining in Bioinformatics, Genome Kenkyuu
Jikken Handbook, pp. 45-48, Yodosha, 2004. (In Japanese. See my Japanese publication list). (publisher's site)
Book Editor/Guest Editorial
- Tetsuo Shibuya, Chuan Yi Tang, Paul Horton, Kiyoshi Asai: Guest Editorial
for the 25th International Conference on Genome Informatics (GIW/ISCB-Asia
2014). IEEE/ACM Trans. Comput. Biology Bioinform. 12(4): 761-762 (2015).
- Tetsuo Shibuya, Chuan Yi Tang, Paul Horton, Kiyoshi Asai: Editorial. J.
Bioinformatics and Computational Biology 12(6) (2014)
- Tetsuo Shibuya, Hisashi Kashima, Jun Sese, and Shandar Ahmad (Eds): Pattern
Recognition in Bioinformatics - 7th IAPR International Conference, PRIB
2012. LNCS 7632, Springer, 2012.
Invited Journal Articles
- Tetsuo Shibuya, Faster Big Data Searching via Statistical Model-based Algorithm
Design, Journal of the Institute of Electronics, Information and Communication
Engineers, vol. 97, No. 5, May 2014, pp. 384-387. (In Japanese, see my Japanese publication list)
- Tetsuo Shibuya, Current Bioinformatics and Its Future, Journal of the Institute
of Electronics, Information and Communication Engineers, vol. 90, no. 2,
2007, pp. 145-147. (In Japanese, see my Japanese publication list)
- Tetsuo Shibuya, BDGF Method, Bio Venture, 2(6), pp. 86-89, 2002. (In Japanese,
see my Japanese publication list)
Keynotes/Invited Talks
- Tetsuo Shibuya, "Differentially Private Methods in Bioinformatics",
Combinatorial Problems of Strings and Graphs and Their Applications in
Bioinformatics, Part 2, April 6, 2022, Singapore.
- Tetsuo Shibuya, "Algorithmic Challenges for Biomedical Big Data",
Keynote, The 11th International Conference on Bioscience, Biochemistry
and Bioinformatics, 2021, January 9-12, 2021.
- Tetsuo Shibuya Succinct Data Structure Applications, The 5th International
Workshop on Innovative Algorithms for Big Data, October 30, 2019.
- Tetsuo Shibuya, Algorithmic Challenges for Bio Big Data, UTokyo-IITM Workshop, March 15th, 2017, Chennai, India.
- Tetsuo Shibuya, Algorithm Design Paradigm Shift Needed for Bio Big Data,
Genomic Medicine 2015, Ho Chi Minh, Vietnam, July 21, 2015.
- Tetsuo Shibuya, Algorithmic Challenges to Bio Big Data, The 11th International
Workshop on Advanced Genomics, Tokyo, Japan, May 22, 2015.
- Tetsuo Shibuya, Designing Faster Algorithms For Big Data, UK-Japan Workshop
on Big Data, February 6, 2014.
- Tetsuo Shibuya, Protein Structure Comparison Algorithms, The 35th Annual
Meeting of the Molecular Biology Society of Japan, December 13, 2012. (In
Japanese, see my Japanese publication list)
- Tetsuo Shibuya, Large-Scale Informtaion Technologies for Next Generation
Sequencers, The 56th Annual Meeting of the Japan Society of Human Genetics,
November 10, 2011. (In Japanese, see my Japanese publication list)
- Tetsuo Shibuya, Statistical Model-based Algorithm Design Framework for
Faster Protein Structure Database Searching, Keynote, The 2010 Annual Conference
of the Japanese Society for Bioinformatics (JSBi 2010), December 13-15,
2010.
- Tetsuo Shibuya, Large-Scale Computation Platform for Cancer Whole Genome
Analysis, The 55th Annual Meeting of the Japan Society of Human Genetics,
October 28, 2010. (In Japanese, see my Japanese publication list)
- Tetsuo Shibuya, Next-Generation Cancer Genome Analysis Pipeline, 2nd NUS-UT
Workshop on Computational Systems Biology, Plenary Lecture, February 2010.
- Tetsuo Shibuya, Protein Structures and Combinatorial Pattern Matching.
SIG FPAI-68, 2008. (In Japanese, see my Japanese publication list)
- Tetsuo Shibuya, Combinatorial Structural Pattern Matching, The Second Japan-Taiwan
Bilateral Symposium on Bioinformatics, November 7-9, 2006.
- Tetsuo Shibuya, Indexing Structures for Biomolecular Structures, The First
Japan-Taiwan Bilateral Symposium on Bioinformatics, March 13-15, 2006.
Invited Seminar Talks
- Tetsuo Shibuya, Algorithm-driven Science, Symposium on Mathematics, Algorithms,
Compter Science, and Data Science, June 10, Tokyo, 2017. (In Japanese,
see my Japanese publication list)
- Tetsuo Shibuya, Algorithms in the Big Genomic Data Era, The 46th Workshop,
The 164th Committee on Genome Technology, Japan Society for the Promotion
of Science, October 24, 2014. (In Japanese, see my Japanese publication list)
- Tetsuo Shibuya, Faster Protein Structure Database Searching by a New Indexing
Data Structure, CREST Symposium, January 12, 2014. (In Japanese, see my Japanese publication list)
- Tetsuo Shibuya, Indexing Protein 3-D Structures for Faster Similarity Search,
November 29-30, Exploring the Limits of Computation (ELC), November 29-30,
2013.
- Tetsuo Shibuya, Indexing Protein 3-D Structures for Faster Structural Similarity
Queries, Seminar at Bioinformatics Center, Institute for Chemical Research,
Kyoto University, October 18, 2013.
- Tetsuo Shibuya, Fast Indexing Methods for Protein 3-D Structure Searching,
NII Shonan Seminar 29: Compact Data Structures for Big Data, 2013.
- Tetsuo Shibuya, Future Algorithm Design for Indexing in the Genome Big-Data
Era, GCOE Seminar, Decipherring Biosphere from Genome Big Bang, March 1,
2013. (In Japanese, see my Japanese publication list)
- Tetsuo Shibuya, Succinct Representations of Assembly Graphs, The 164th
Committee on Genome Technology, Japan Society for the Promotion of Science,
January 11, 2013.
- Tetsuo Shibuya, Statistical Models and Large-Scale Pattern Matching Algorithms,
Minato Discrete Structure Manipulation System Project Seminar, January
20, 2012. (In Japanese, see my Japanese publication list)
- Akihiro Fujimoto, Tetsuo Shibuya, "Information Analysis at the ICGC",
The 34th Workshop, The 164th Committee on Genome Technology, Japan Society
for the Promotion of Science, September 10, 2010. (In Japanese, see my Japanese publication list)
- Tetsuo Shibuya, A New Algorithm Design Framework for Searching Protein
3-D Structures, GCOE (Decipherring Biosphere from Genome Big Bang) Special
Lecture, 2010. (In Japanese, see my Japanese publication list)
- Tetsuo Shibuya, Combinatorial Pattern Matching for Protein 3-D Structures,
SEQUOIA seminar, INRIA, 2008.
- Tetsuo Shibuya, Indexing Technologies and Its Application to Gene Finding,
Seimei-Jouhou-Kagaku Special Seminar, CBRC, Advanced Industrial Science
and Technology, November 20, 2002. (In Japanese, see my Japanese publication list)
- Tetsuo Shibuya, Pattern Discovery and Mining in Large Databases, BioEXPO
2002. Senmon-Gijutsu Seminar, July 12, 2002. (In Japanese, see my Japanese publication list)
- Tetsuo Shibuya, New Approaches to Flexible Alignment of Multiple Biological
Sequences, Combinatorial Optimization Seminar: Theory and Applications
(COSTA), 97-4, October 25, 1997. (In Japanese, see my Japanese publication list)
Invited Conference Panel Discussions
- Antonia Kwan, Satoru Miyano, Yasushi Okazaki and Tetsuo Shibuya, What are
the applications and limitations of microarray datamining for immunology?
First International Immunoinformatics Symposium, February 26, 2004.
Refereed Conference Posters
- Ritsuko Onuki, Tetsuo Shibuya, and Minoru Kanehisa, Haplotype Inference
Probability-based Genotype Clustering, Proc. 7th Annual Workshop on Bioinformatics
and Systems Biology (IBSB), Genome Informatics, Vol. 18, pp. 26-27, 2007.
- Makoto Kano, Hisashi Kashima, Tetsuo Shibuya, Kaori Ide, Aiko Kashihara,
Noriko Nakagawa, Seiki Kuramitsu, Mariko Hatakeyama, and Akihiko Konagaya,
Method for Normalization of Gene Expression Data, Genome Informatics, Vol.
14, p. 336-337, 2003.
- Tetsuo Shibuya and Hiroshi Imai, Suboptimal Alignments of Multiple Biological Sequences. Intelligent Systems on Molecular Biology '96, Book of Abstracts, p. 76, June 1996.
Non-refereed Technical Reports / Talks
- Arda Akdemir, Tetsuo Shibuya, UDON: Unsupervised Data SelectiON for Biomedical Entity Recognition, The 27th East Asia Joint Symposium, October 27-29, 2021.
- Akito Yamamoto, Tetsuo Shibuya, Efficient Differentially Private Methods
for a Transmission Disequilibrium Test, IPSJ SIGBIO-67, September 30, 2021.
(SIGBIO Good Presentation Award)
- Sasaki et al, IPSJ, 2017. (In Japanese, see Japanese publications)
- Taku Onodera, Tetsuo Shibuya, LA 2016, July 20, 2016, Nara. (In Japanese,
see Japanese publications)
- Yang Li, Tetsuo Shibuya, Malphite: A Convolutional Neural Network and Ensemble
Learning Based Protein Secondary Structure Predictor, IPSJ SIG Technical
Report, 2015-BIO-44(1), December 7, 2015.
- Yoichi Sasaki, Tetsuo Shibuya, Kimito Ito, Hiroki Arimura, Efficient Approximate
3-Dimensional Point Set Matching and Its Application to Molecular
Pattern Matching, IPSJ SIG Technical Report, 2015-BIO-42(68), pp. 1-7,
June 15, 2015. (SIGBIO Best Student Presentation Award)
- Taku Onodera, Kunihiko Sadakane, and Tetsuo Shibuya, Detecting Superbubbles
in Assembly Graphs, IPSJ SIG Technical Report, 2013-BIO-35(4), 2013
- Alexander Bowe, Taku Onodera, Kunihiko Sadakane and Tetsuo Shibuya, A New
Implementation of Succinct de Bruijn Graphs, The 6th Annual Meeting of
Asian Association for Algorithms and Computation, 2013.
- Alexander Bowe, Taku Onodera, Kunihiko Sadakane and Tetsuo Shibuya, Experimental
Results on Succinct de Bruijn Graphs, The 16th Korea-Japan Joint Workshop
on Algorithms and Computation, 2013.
- Taku Onodera and Tetsuo Shibuya, IPSJ SIG Technical Report, 2012-BIO-31(4),
2012.
- Alexander Bowe, Taku Onodera, Kunihiko Sadakane and Tetsuo Shibuya, Compression
of de Bruijn graphs, Technical Report of IEICE, COMP, September 2012.
- Alexander Bowe, Taku Onodera, Kunihiko Sadakane and Tetsuo Shibuya, Implementation
of Succinct de Bruijn Graphs, Proc. 3rd Workshop on Algorithms for Large-Scale
Information Processing (ALSIP 2012), 2012.
- Taku Onodera and Tetsuo Shibuya, An Index Structure for Spaced Seed Search,
IPSJ SIG Technical Report, 2011-AL-137(2), 2011.
- Tetsuo Shibuya, Linear-Time Algorithm for Searching Protein 3-D Structures,
IPSJ SIG Notes SIGAL 123-4, pp. 25-32, 2009.
- Koichi Suematsu, Tetsuo Shibuya, Flexible Protein Alignment of 3D-Structures
Allowing Dynamic Transformation, ISPSJ SIG Notes SIGBIO 12-12, pp. 87-94,
2008.
- Tetsuo Shibuya, Efficient Substructure RMSD Query Algorithms, IPSJ SIG
Notes SIGAL 114-8, pp. 57-64, 2007.
- Tetsuo Shibuya, Fast and Accurate Algorithms for Protein Hinge Detection,
IPSJ SIG Notes SIGBIO 10-4, pp. 25-32, 2007.
- Tetsuo Shibuya, Prefix-Shuffled Geometric Suffix Tree, IPSJ SIG Notes SIGAL 112-1, 2007, pp. 1-8.
- Kohichi Suematsu, Michihiro Araki, and Tetsuo Shibuya, Graph tiling algorithm
for molecular synthesis analysis, SIGAL 106-4, pp. 25-32, 2006.
- Tetsuo Shibuya, Geometric Suffix Tree: A New Index Structure for Protein
3-D Structures, IPSJ SIG Notes SIGAL 105-3, pp. 17-24, 2006.
- Tetsuo Shibuya, and Igor Kurochkin, Match Chaining Algorithms for cDNA
Mapping. Technical Report of IEICE, Vol. 103, No. 326, COMP2003-37, pp.
1-8, 2003.
- Tetsuo Shibuya, Christian Schoenbach, Hisashi Kashima and Akihiko Konagaya,
Accurate cDNA Clustering Algorithm based on Spliced Sequence Alignment,
Technical Report of IEICE, COMP2002-11, pp. 17-24, May 26, 2002.
- Tien Huynh, Isidore Rigoutsos, Laxmi Parida, Daniel Platt and Tetsuo Shibuya,
The IBM Bioinformatics Group Web Server - Tools and Content, IBM Technical
Report RC22726, 2002
- Tetsuo Shibuya and Isidore Rigoutsos, Motif Search Algorithm and Its Applications
for Gene Finding, Technical Report of IEICE, Vol. 101, No. 376, COMP2001-48,
pp. 85-92, 2001.
- Tetsuo Shibuya and Isidore Rigoutsos, Dictionary-driven Microbial Gene
Finding, IBM Technical Report RC22051, 2001.
- Tetsuo Shibuya, Generalization of a Suffix Tree for RNA Structural Pattern
Matching, IBM TRL Report RT0342, 2000.
- Tetsuo Shibuya, New Approaches for Analyzing Recombinations of Biological Sequences, IBM TRL Report RT0343, 2000.
- Tetsuo Shibuya, Constructing the Suffix Tree of a Tree with a Large Alphabet,
IPSJ SIG Notes SIGAL 69-4, pp. 25-32, 1999.
- Tetsuo Shibuya, New Approaches for Analyzing Recombinations of Biological
Sequences, Technical Report of IEICE, Vol. 99, No. 30, COMP99-1, pp. 1-8,
1999.
- Hiroshi Kawazoe, Tetsuo Shibuya, Takeshi Tokuyama, Optimal On-line Algorithms
for an Electronic Commerce Money Distribution System, IBM TRL Report RT0317,
1999.
- Tetsuo Shibuya, Constructing the Suffix Tree of a Tree with a Large Alphabet,
IBM TRL Report RT0320, 1999.
- Hiroshi Kawazoe, Tetsuo Shibuya, and Takeshi Tokuyama, Optimal On-line
Algorithms for an Electronic Commerce Money Distribution System, Technical
Report of IEICE, Vol. 98, No. 283, COMP98-32, pp. 17-24, 1998.
- Tetsuo Shibuya, Computing the n x m Shortest Paths Efficiently By Using
the A* Algorithm, IPSJ SIG Notes SIGAL 62-2, pp. 9-16, 1998.
- Tetsuo Shibuya and Hiroshi Imai, New Approaches to Flexible Alignment of Multiple Biological Sequences, Cooperative Research Report, "Modeling and Algorithms 9", The Institute of Statical Mathematics, 1997.
- Tetsuo Shibuya, Computing the n x m Shortest Paths Efficiently By Using
the A* Algorithm, IBM TRL Report RT5133. 1997.
- Tetsuo Shibuya and H. Imai, On Parametric Alignments of Multiple Biological
Sequences, IPSJ SIG Notes SIGAL52-4, IPSJ, pp. 25-32, 1996, In Japanese.
- Tetsuo Shibuya and Hiroshi Imai, Suboptimal Alignments of Multiple Biological
Sequences, IPSJ SIG Notes SIGAL51-1, IPSJ, pp. 1-8, 1996.
- Hiroshi Imai and Tetsuo Shibuya, K-opt Algorithm for Multiple Alignment, Cooperative Research Report, "Modeling and Algorithms 8", The Institute of Statical Mathematics, 1996.
- Tetsuo Shibuya, Finding the k Shortest Paths by AI Search Techniques, Cooperative
Research Report, "Modeling and Algorithms 7", The Institute of
Statical Mathematics, Vol.77, pp. 212-222, 1995.
Non-refereed Poster Presentation
- Yao-zhong Zhang, Arda Akdemir, Georg Tremmel, Seiya Imoto, Satoru Miyano,
Tetsuo Shibuya, Rui Yamaguchi, Nanopore base-calling from a perspective
of instance segmentation, ISMB-ECCB 2019.
- Kiyoshi Yamaguchi, Mitsuhiro Komura, Eigo Shimizu, Shinichi Kasuya, Rui
Yamaguchi, Tetsuo Shibuya, Seiya Imoto, Satoshi Nagayama, Norihiko Takahashi,
Tsuneo Ikenoue, Sumio Sugano, Satoru Miyano, Yoichi Furukawa, Search for
pathogenic variants in familial colorectal cancer using a next generation
sequencer, The 73rd Annual Meeting of the Japanese Cancer Association,
S20-4, 2014.
- Alexander Bowe, Taku Onodera, Kunihiko Sadakane and Tetsuo Shibuya, Implementation
of Succinct de Bruijn Graphs, The 12th Workshop on Algorithms in Bioinformatics,
2012.
- Akihiro Fujimoto, Hidwaki Nakagawa, Naoya Hosono, Kaoru Nakano, Tetsuo
Abe, Masao Nagasaki, Rui Yamaguchi, Tetsuo Shibuya, Michiaki Kubo, Satoru
Miyano, Usuke Nakamura and Tatsuhiko Tsunoda, Construction of analysis
pipeline and accurate variant calls of a Japanese individual using massively
parallel sequencing, The 2nd Biosupercomputing symposium, P-52, p. 146,
2010.
- Tetsuo Shibuya, Faster Structural Pattern Matching Algorithms, The 9th
International Workshop on Bioinformatics and Systems Bilogy, 2009.
- Ritsuko Onuki, Tetsuo Shibuya, and Minoru Kanehisa, A New Method for Genotype
Clustering based on Haplotype Inference, Biochemistry and Molecular Biology
(BMB 2007), 1P-1071, 2007.
- Ritsuko Onuki, Tetsuo Shibuya, and Minoru Kanehisa, Genotype Clustrering
based on Haplotype Inference Probabilities, The 52nd Annual Meeting of
the Japan Society of Human Genetics, 2007.
- Yoshihiro Ohta and Tetsuo Shibuya, Extracting Causalities in Large Biological
Data Sets, Japanese Society of Molecular Biology, 1998 Annual meeting,
December 1999, Yokohama.
Theses
- Tetsuo Shibuya, Research on Fast Algorithms for Comparison and Indexing
of Biological Sequence Information, Ph. D Thesis, Department of Information
Science, Faculty of Science, University of Tokyo, December 2002. (UT Repository)
- Tetsuo Shibuya, New Approaches to Flexible Alignment of Multiple Biological
Sequences, Master Thesis, Deptartment of Infomation Science, Faculty of
Science, University of Tokyo, February 1997.
- Tetsuo Shibuya, Finding the k shortest paths by AI search techniques. Bachelor
Thesis, Deptartment of Infomation Science, Faculty of Science, University
of Tokyo, February 1995.
Others
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